[2024-01-24 15:18:27,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference
[2024-01-24 15:18:28,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,957] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg08e2ae14-4b21-496b-a2e8-96d98235eab2/GCF_003697785.1_ASM369778v1_genomic.fna.gz | prodigal -d GCF_003697785.1_ASM369778v1_genomic.fna/cds.fna -a GCF_003697785.1_ASM369778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:43,611] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:43,611] [INFO] Task started: HMMsearch
[2024-01-24 15:18:43,611] [INFO] Running command: hmmsearch --tblout GCF_003697785.1_ASM369778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/reference_markers.hmm GCF_003697785.1_ASM369778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:43,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:43,916] [INFO] Found 6/6 markers.
[2024-01-24 15:18:43,960] [INFO] Query marker FASTA was written to GCF_003697785.1_ASM369778v1_genomic.fna/markers.fasta
[2024-01-24 15:18:43,960] [INFO] Task started: Blastn
[2024-01-24 15:18:43,960] [INFO] Running command: blastn -query GCF_003697785.1_ASM369778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/reference_markers.fasta -out GCF_003697785.1_ASM369778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:44,955] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:44,959] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:44,959] [INFO] Target genome list was writen to GCF_003697785.1_ASM369778v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:44,966] [INFO] Task started: fastANI
[2024-01-24 15:18:44,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e2ae14-4b21-496b-a2e8-96d98235eab2/GCF_003697785.1_ASM369778v1_genomic.fna.gz --refList GCF_003697785.1_ASM369778v1_genomic.fna/target_genomes.txt --output GCF_003697785.1_ASM369778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:58,431] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:58,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:58,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:58,445] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:58,445] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:58,446] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	81.7522	701	1535	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	81.6468	747	1535	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	81.4812	804	1535	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.1041	655	1535	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.4347	570	1535	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	80.3236	532	1535	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.3066	594	1535	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	80.2689	648	1535	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	80.0905	570	1535	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	79.9713	576	1535	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.9343	594	1535	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	79.8442	546	1535	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	79.7961	559	1535	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	79.6482	561	1535	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	79.5828	544	1535	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.9705	522	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:58,447] [INFO] DFAST Taxonomy check result was written to GCF_003697785.1_ASM369778v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:58,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:58,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:58,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/checkm_data
[2024-01-24 15:18:58,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:58,495] [INFO] Task started: CheckM
[2024-01-24 15:18:58,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003697785.1_ASM369778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003697785.1_ASM369778v1_genomic.fna/checkm_input GCF_003697785.1_ASM369778v1_genomic.fna/checkm_result
[2024-01-24 15:19:44,774] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:44,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:44,797] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:44,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:44,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003697785.1_ASM369778v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:44,798] [INFO] Task started: Blastn
[2024-01-24 15:19:44,798] [INFO] Running command: blastn -query GCF_003697785.1_ASM369778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a2b0284-ec19-40fa-a80a-271985ef31e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003697785.1_ASM369778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:46,492] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:46,495] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:46,495] [INFO] Target genome list was writen to GCF_003697785.1_ASM369778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:46,501] [INFO] Task started: fastANI
[2024-01-24 15:19:46,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg08e2ae14-4b21-496b-a2e8-96d98235eab2/GCF_003697785.1_ASM369778v1_genomic.fna.gz --refList GCF_003697785.1_ASM369778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003697785.1_ASM369778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:54,510] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:54,524] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:54,524] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003697785.1	s__Paracoccus alkanivorans	100.0	1533	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003007735.2	s__Paracoccus marinus_A	88.9237	972	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156835.1	s__Paracoccus saliphilus	86.8731	983	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	81.8692	657	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	81.6557	746	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900110285.1	s__Paracoccus alcaliphilus	81.1022	655	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056335.1	s__Paracoccus indicus	79.7721	562	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	79.6389	562	1535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:54,526] [INFO] GTDB search result was written to GCF_003697785.1_ASM369778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:54,526] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:54,530] [INFO] DFAST_QC result json was written to GCF_003697785.1_ASM369778v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:54,530] [INFO] DFAST_QC completed!
[2024-01-24 15:19:54,530] [INFO] Total running time: 0h1m27s